No BAM/SAM or PAF files

[annerilotter]

Hi, I wanted to ask if I can use this tool if I used the nucmer alignment with SyRI. I do not see the option.

Any help would be much appreciated.

Kind regards

[lrauschning]

Hi @annerilotter,

For parsing alignment files, we use pysam, which does not support delta format.
You might want to try converting .delta into any standard alignment format, using one of the strategies mentioned in mummer4/mummer#80 .
Other than that, the syri output should work much like any other. For realignment, alignment calls will be made to minimap2, although there is experimental support for providing all vs all pairwise alignments in any format (with the --pairwise option).

Hope that helps and feel free to open an issue if there are any other problems – msyd is still under development, so any feedback is welcome!
Leon